[BioC] exonmap question: rma (& plier ) crashes conti.

[Michal Okoniewski]

Hi Tae-Hoon,

The numbers that you get from the size of raw data is strange - for exon 
chip there should be 6553600 rows.
Hmmm... sure that you read in are exon chip CEL files?
The number of probesets in the exon.pmcdf is also different - there are 
normally 1411189.

Cheers,
Michal

Tae-Hoon Chung wrote:
> Hi, All;
>
> I posted this question and someone suggested to update my bioconductor
> packages and retry. I did and retried but failed again:
>
>
>   
>> library(exonmap)
>>     
> Loading required package: affy
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: affyio
> Loading required package: preprocessCore
> Loading required package: simpleaffy
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: RColorBrewer
> Loading required package: RMySQL
> Loading required package: DBI
> Loading required package: plier
>   
>> setwd('~/KCDC/LCL-microarray/scandata')
>> raw <- read.exon(covdesc='design.csv')
>> raw at cdfName <- "exon.pmcdf"
>> dat.rma <- rma(raw)
>>     
> Error in .local(object, ...) : subscript out of bounds
>   
>> sessionInfo()
>>     
> R version 2.7.2 beta (2008-08-16 r46368)
> i386-apple-darwin9.4.0
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] exon.pmcdf_1.1       exonmap_1.6.05       plier_1.10.0
>  [4] RMySQL_0.6-0         DBI_0.2-4            RColorBrewer_1.0-2
>  [7] simpleaffy_2.16.0    gcrma_2.12.1         matchprobes_1.12.0
> [10] genefilter_1.20.0    survival_2.34-1      affy_1.18.2
> [13] preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.2.2 RSQLite_0.6-9       annotate_1.18.0
>
>
> When I traced the source of the error, I got the following result:
>
>   
>> traceback()
>>     
> 4: .local(object, ...)
> 3: pm(object, subset)
> 2: pm(object, subset)
> 1: rma(raw)
>
>
> The problem occurred at the .local function of the following method
> definition:
>
>   
>> showMethods("pm", class="AffyBatch", includeDef=T)
>>     
> Function: pm (package affy)
> object="AffyBatch"
> function (object, ...)
> {
>     .local <- function (object, genenames = NULL, LISTRUE = FALSE)
>     {
>         if (is.null(genenames) & !LISTRUE) {
>             cdfname <- getCdfInfo(object)
>             psets <- as.list(cdfname)
>             psets <- psets[order(names(psets))]
>             index <- unlist(sapply(psets, function(x) x[, 1]),
>                 use.names = FALSE)
>             return(exprs(object)[index, , drop = FALSE])
>         }
>         else {
>             return(probes(object, "pm", genenames, LISTRUE = LISTRUE))
>         }
>     }
>     .local(object, ...)
> }
>
>
> When I followed the steps in the .local function definition myself, I got
> the following result:
>
>
>   
>> psets <- as.list(getCdfInfo(raw))> psets <- psets[order(names(psets))]
>> index <- unlist(sapply(psets, function(x) x[,1]), use.names=F)
>> length(index)
>>     
> [1] 1164743
>   
>> dim(exprs(raw))
>>     
> [1] 1102500      39
>   
>> mat <- exprs(raw)[index, , drop=F]
>>     
> Error: subscript out of bounds
> No suitable frames for recover()
>
>
> >From this, it is obvious that "subscript out of bounds" error happened. (Of
> course!) Is the annotation package at fault or the "pm" method at fault or
> both or neither of them at fault? When I used the "huex10stv2hsentrezgcdf"
> annotation package instead of the "exon.pmcdf" annotation package, the same
> error occurred.
>
> Thanks in advance,
> Tae-Hoon
>
>